We have successfully demonstrated a novel technique based on energy-filtered electron tomography for imaging the three-dimensional distribution of specific chemical elements in cells. This system has been implemented on a 300 kV field-emission transmission electron microscope equipped with an advanced imaging filter including a 2048 x 2048 pixel CCD camera with high detective quantum efficiency and fast read-out. Acquisition is controlled by means of flexible computer scripts, which enable correction for specimen drift and defocus between successive tilt angles and collection of energy-filtered images at defined energy for each tilt angle. Projected phosphorus distributions are obtained by acquiring images above and below the L-edge and by subtracting the extrapolated background intensity at each pixel. The three-dimensional distribution of phosphorus is then obtained using a back-projection algorithm after careful alignment of fiducial gold nanoparticles that are displayed in concurrently acquired zero-loss images. The feasibility of mapping the three-dimensional distribution of DNA in the cell nucleus is now being assessed, as well as the extent to which three-dimensional elemental images can be quantified to determine the numbers of specific atoms per voxel.